Merge pull request #89 from sahilseth/devel

merging devel, with several bug fixes and added features

.Rbuildignore

@@ -7,7 +7,6 @@
 .travis2.yml
 .travis.yml
 
-
 misc
 inst/extdata/*
 inst/staticdocs
@@ -17,6 +16,7 @@ README\.Rmd
 README\.html
 TODO\.md
 cran\-comments\.md
+CONTRIBUTING.md
 
 ## ignore test files and folders
 tests/testthat/Rplots.pdf

.travis.yml

@@ -1,30 +1,15 @@
-## Sample .travis.yml file for use with metacran/r-builder
-## See https://github.com/metacran/r-builder for details.
+# https://docs.travis-ci.com/user/languages/r/
+language: r
 
-language: c
-sudo: required
+# cache dep packages
+cache: packages
+warnings_are_errors: false
 
-before_install:
-  - curl -OL https://raw.githubusercontent.com/metacran/r-builder/master/pkg-build.sh
-  - chmod 755 pkg-build.sh
-  - ./pkg-build.sh bootstrap
+r_packages: 
+  - openxlsx
+  - ggplot2
 
-install:
-  - ./pkg-build.sh install_deps
-
-script:
-  - ./pkg-build.sh run_tests
-
-after_failure:
-  - ./pkg-build.sh dump_logs
-
-notifications:
-  email:
-    on_success: change
-    on_failure: change
-
-env:
-  matrix:
-    - RVERSION=oldrel
-    - RVERSION=release
-    - RVERSION=devel
+r:
+  - oldrel
+  - release
+  - devel

.travis_bak.yml

@@ -0,0 +1,30 @@
+## Sample .travis.yml file for use with metacran/r-builder
+## See https://github.com/metacran/r-builder for details.
+
+language: c
+sudo: required
+
+before_install:
+  - curl -OL https://raw.githubusercontent.com/metacran/r-builder/master/pkg-build.sh
+  - chmod 755 pkg-build.sh
+  - ./pkg-build.sh bootstrap
+
+install:
+  - ./pkg-build.sh install_deps
+
+script:
+  - ./pkg-build.sh run_tests
+
+after_failure:
+  - ./pkg-build.sh dump_logs
+
+notifications:
+  email:
+    on_success: change
+    on_failure: change
+
+env:
+  matrix:
+    - RVERSION=oldrel
+    - RVERSION=release
+    - RVERSION=devel

DESCRIPTION

@@ -6,7 +6,7 @@ Description: This framework allows you to design and implement complex
     been built keeping in mind the needs of bioinformatics workflows. However, it is
     easily extendable to any field where a series of steps (shell commands) are to
     be executed in a (work)flow.
-Version: 0.9.10.9022
+Version: 0.9.10.9027
 Depends:
     R (>= 3.0.2),
     methods,
@@ -23,10 +23,12 @@ Suggests:
     funr
 Enhances:
     ggplot2,
-    openxlsx
+    openxlsx,
+    pacman,
+    cowplot
 VignetteBuilder: knitr
 URL: https://github.com/sahilseth/flowr
 BugReports: https://github.com/sahilseth/flowr/issues
 Authors@R: c(person("Sahil", "Seth", role = c("aut", "cre"), email = "me@sahilseth.com"))
 License: MIT + file LICENSE
-RoxygenNote: 5.0.1
+RoxygenNote: 6.1.1

NAMESPACE

@@ -41,6 +41,8 @@ export(fetch_pipes)
 export(flow)
 export(flowopts)
 export(get_opts)
+export(get_resources)
+export(get_resources_lsf)
 export(get_status)
 export(get_unique_id)
 export(get_wds)
@@ -56,6 +58,7 @@ export(queue)
 export(rerun)
 export(run)
 export(run_pipe)
+export(run_pipe_v2)
 export(set_opts)
 export(setup)
 export(status)

NEWS.md

@@ -24,6 +24,14 @@ source: "github.com/sahilseth/flowr/tree/devel/NEWS.md"
 <br>
 
 
+flowr 0.9.11
+----------------------------------------------
+> 2019-04-01
+
+* bugfix in for `moab` and `sge` schedulers (see #74 for details)
+
+
+
 flowr 0.9.10.9022
 ----------------------------------------------
 > 2017-04-30